Afternoon thunderstorms (TSs) over the Taipei metropolitan area often cause meteorological disasters. Further understanding of essential factors for TS organization is important for improving prediction accuracy. This study conducts numerical simulations in two real situations with different environmental profiles: a heavy rainfall (TS) case and a no rainfall (NoTS) case. The TS simulation reasonably captures the afternoon rainfall in the Taipei basin. The thermal structure and sea breeze evolution in the simulations are verified by the observation from a field campaign. In both cases, the sea breeze develops in the afternoon. Weak environmental flow and high humidity are observed in the TS case. In contrast, a thick and dry layer with southeasterly wind above 2-km height is presented in the NoTS case. Four idealized experiments are then performed with the initial conditions based on the actual TS/NoTS soundings and with/without the southeasterly environmental flows. Despite the different thermal profiles, the two simulations without the southeasterly flows exhibit qualitatively similar rainfall distribution and the evolution of the sea breeze to that of the real TS simulation. However, with the southeasterly environmental flows, the simulation with the NoTS sounding exhibits considerably less convection and rainfall. Therefore, not only moisture profiles but also environmental wind profiles are critical to the TS organization. Novelly, this study further shows that the environmental flow contributes to the suppression of afternoon TSs through keeping entrainment due to the continuous supply of the dry airmass.